(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.soe.ucsc.edu/research/compbio/sam.html
Citations (SAM, SAM-T99, HMMs)
- R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
- K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
- A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
Sequence numbers correspond to the following labels:
-
-
- gi|29341004|gb|AAO78794.1|_1:122 conserved hypothetical protein [Bacteroides thetaiotaomicron VPI-5482]
- gi|29349097|ref|NP_812600.1| hypothetical protein BT3689 [Bacteroides thetaiotaomicron VPI-5482]
-
- gi|60491430|emb|CAH06180.1|_1:122 conserved hypothetical protein [Bacteroides fragilis NCTC 9343]
- gi|60679996|ref|YP_210140.1| hypothetical protein BF0416 [Bacteroides fragilis NCTC 9343]
-
- gi|52214628|dbj|BAD47221.1|_1:122 conserved hypothetical protein [Bacteroides fragilis YCH46]
- gi|53711763|ref|YP_097755.1| hypothetical protein BF0472 [Bacteroides fragilis YCH46]
-
- gi|89894028|ref|YP_517515.1|_1:122 hypothetical protein DSY1282 [Desulfitobacterium hafniense Y51]
- gi|89333476|dbj|BAE83071.1| hypothetical protein [Desulfitobacterium hafniense Y51]
- gi|109646405|ref|ZP_01370309.1| conserved hypothetical protein [Desulfitobacterium hafniense DCB-2]
- gi|109641651|gb|EAT51205.1| conserved hypothetical protein [Desulfitobacterium hafniense DCB-2]
-
- gi|88946180|ref|ZP_01149267.1|_1:123 conserved hypothetical protein [Desulfotomaculum reducens MI-1]
- gi|88924302|gb|EAR43305.1| conserved hypothetical protein [Desulfotomaculum reducens MI-1]
-
- gi|15644920|ref|NP_207090.1|_2:116 hypothetical protein HP0292 [Helicobacter pylori 26695]
- gi|2313390|gb|AAD07362.1| predicted coding region HP0292 [Helicobacter pylori 26695]
-
- gi|4154812|gb|AAD05868.1|_2:116 putative [Helicobacter pylori J99]
- gi|15611347|ref|NP_222998.1| hypothetical protein jhp0277 [Helicobacter pylori J99]
-
- gi|34482315|emb|CAE09316.1|_2:122 conserved hypothetical protein [Wolinella succinogenes]
- gi|34556601|ref|NP_906416.1| hypothetical protein WS0153 [Wolinella succinogenes DSM 1740]
-
- gi|107836492|gb|ABF84361.1|_2:116 hypothetical protein HPAG1_0294 [Helicobacter pylori HPAG1]
- gi|108562719|ref|YP_627035.1| hypothetical protein HPAG1_0294 [Helicobacter pylori HPAG1]
-
- gi|32263060|gb|AAP78106.1|_2:122 conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
- gi|32267008|ref|NP_861040.1| hypothetical protein HH1509 [Helicobacter hepaticus ATCC 51449]
-
- gi|109947143|ref|YP_664371.1|_2:116 conserved hypothetical protein [Helicobacter acinonychis str. Sheeba]
- gi|109714364|emb|CAJ99372.1| conserved hypothetical protein [Helicobacter acinonychis str. Sheeba]
-
- gi|28210530|ref|NP_781474.1|_10:134 hypothetical protein CTC00813 [Clostridium tetani E88]
- gi|28202967|gb|AAO35411.1| conserved protein [Clostridium tetani E88]
-
- gi|90573858|ref|ZP_01230366.1|_3:122 hypothetical protein CdifQ_02002724 [Clostridium difficile QCD-32g58]
-
- gi|34541455|ref|NP_905934.1|_3:127 hypothetical protein PG1841 [Porphyromonas gingivalis W83]
- gi|34397772|gb|AAQ66833.1| conserved hypothetical protein [Porphyromonas gingivalis W83]
-
- gi|19713732|gb|AAL94483.1|_2:116 Hypothetical protein [Fusobacterium nucleatum subsp. nucleatum ATCC 25586]
- gi|19703622|ref|NP_603184.1| hypothetical protein FN0277 [Fusobacterium nucleatum subsp. nucleatum ATCC 25586]
-
- gi|67916587|ref|ZP_00510291.1|_1:126 conserved hypothetical protein [Clostridium thermocellum ATCC 27405]
- gi|67849451|gb|EAM45058.1| conserved hypothetical protein [Clostridium thermocellum ATCC 27405]
-
- gi|46450378|gb|AAS97026.1|_4:118 conserved hypothetical protein [Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough]
- gi|46580958|ref|YP_011766.1| hypothetical protein DVU2554 [Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough]
-
- gi|34762805|ref|ZP_00143791.1|_2:116 hypothetical protein [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
- gi|27887507|gb|EAA24591.1| hypothetical protein [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
-
- gi|21226283|ref|NP_632205.1|_6:120 hypothetical protein MM0181 [Methanosarcina mazei Go1]
- gi|20904527|gb|AAM29877.1| conserved protein [Methanosarcina mazei Go1]
-
- gi|82501163|ref|ZP_00886531.1|_2:119 conserved hypothetical protein [Caldicellulosiruptor saccharolyticus DSM 8903]
- gi|82400837|gb|EAP41690.1| conserved hypothetical protein [Caldicellulosiruptor saccharolyticus DSM 8903]
-
- gi|78193195|gb|ABB30962.1|_13:123 conserved hypothetical protein [Geobacter metallireducens GS-15]
- gi|78221940|ref|YP_383687.1| hypothetical protein Gmet_0720 [Geobacter metallireducens GS-15]
-
- gi|39982913|gb|AAR34372.1|_8:119 conserved hypothetical protein [Geobacter sulfurreducens PCA]
- gi|39996148|ref|NP_952099.1| hypothetical protein GSU1046 [Geobacter sulfurreducens PCA]
10 20 30 40 50 60
| | | | | |
1 MIPFKDITLADRDTITAFTMKSDRRNCDLSFSNLCSWRFLYDTQFAVIDDFLVFKFWAGEQ..LA
2 MIPFKDITLADRDTITAFTMKSDRRNCDLSFSNLCSWRFLYDTQFAVIDDFLVFKFWAGEQ..LA
3 MIAFRDITIQDKDTITAYTMNSCRRNCDLSFSNLCSWRFLYHTKFAIINNFLVFKFWAGDE..LA
4 MIAFRDITIQDKDTITAYTMNSCRRNCDLSFSNLCSWRFLYHTKFAIINNFLVFKFWAGDE..LA
5 MIDFKKIEMRDKEWVKPLLEAADLGGCHQNFTNLFSWSGTYHYQVAQVEDYLVIKGRLGET..YY
6 MINFKKVELADKQWMGPLITLGEMSSSHQNFTNIFAWSEIYHYRVARVSDYLVVKGRLQNGe.QY
7 ---FEKITLAHKDLFSRFLSAQKIVLSDVSFTNCFLWQHARLIQVAVIRDCLVIQTTYENQk.PF
8 ---FEEITLAHKDLFSRFLQTQKIVLSDVSFTNCFLWQHARLIQVAVIRDCLVIQTTYENQk.PF
9 --QWKPIDIEDRETLEGFFRSEELSVSDFSFTNLYLWHFSRSISYAIIEDLLCIKTQYHGEh.PF
10 ---FEKITLAHKDLFSRFLSTQKIVLSDVSFTNCFLWQHARLIQVAVIRDCLVIQTTYENQk.PF
11 --EFKKIELEDRTLLEPFTNQKGRWLSDMNFSNMFMWRHSREISYTFLQEHLIVQTRYPHQn.PF
12 ---FEKLKLEHKDLFSRFLSAQKIVLSDVSFTNCFLWQHARLIRVAVIKDCLVIQTTYENQq.PF
13 MLQFSPLTLEDKEIFDKYIKPYKFKTSEYSFTNQYLWRKGSDVTYTILNDVLIIKKVDYDG..TT
14 ---FKDIELNSKKELDPYFDLVDYEACEYCFSTLYMWQHVYKTGYYIGEDFAVLVGEYEGD..SF
15 -IKFKPVEPADRSAITTITFSSVARICDLAFSNLYCWSFVYGTSWAIVEGCLIIRFKPKSRshPV
16 ---WQKLTIESKSSIEEYT-KNRFEICDLSFSNLLLWSIGENTEYEIENDVLTIRSVYMGD..VY
17 MLDFKPIELKDRELFHEYLKDYDFLTYEYSFLTLYIWRKMYNTEFAIVDDTIVIKKRTANN..GT
18 -TDFSPVTLDAMQDYLALFARTPRRASDYSFTNLWGWAEHYGLEWRFEHGLCWLRQTLPEV..RY
19 ---WQKLTIESKSSIEEYT-KNRFEICDLSFSNLLLWSTGENTEYEIENDVLTIRSVYMGE..VY
20 --DFKPVTLADREFFERHSELYPQTHSSNTFTNMVCWNHFTQYRYAYVNGNIIISGTTGGI..TR
21 --KFYKIDISDKRIFDEYFKAFQPEIADLTFTNLFMWDPFYDINFTEEDGFLLIMAKPYNQ..PP
22 ---ARPLFLADKPFFAAVFAELQPRVSELTFANLYLFREAHDYRLTRVGDSPVVLGKGYDG..EE
23 --DSRPLALADKPLLDALFTELQPRVSELTFANLYLFRGIHDYRLTRLGDALVVLGRGYGG..EA
70 80 90 100 110 1
| | | | |
1 YM...MPVGNGD.LKAV..LRKLIED....ADKEKHNFCMLGVCSNMRADLEAILPERFIFTEDR
2 YM...MPVGNGD.LKAV..LRKLIED....ADKEKHNFCMLGVCSNMRADLEAILPERFIFTEDR
3 YM...MPVGEGN.LEEV..LNELIED....ARQEGEPFCMLGVCSCMREDLEAIMPGQFGFTVDR
4 YM...MPVGEGN.LEEV..LNELIED....ARQEGEPFCMLGVCSCMREDLEAIMPGQFGFTVDR
5 YF...YPAGTGD.VQPV..LEAMKKD....AQENGHEFIVLGISPENMATLKELYPEHFEYEEMR
6 YF...YPAGKGD.PKSV..IETMKQD....AADCGHKFIMLGVSPENIIVLNSLFPESFEYKEMR
7 YF...YPIGKNA.FECV..KELL---....--KLEKNLRFHSLTLEQKDDLKDNFVGVFDFTYNR
8 YF...YPIGKRP.HECV..KELL---....--ELEKNLRFHSLTLEQKDDLKDNFVGVFDFTYNR
9 LF...FPLGKGE.KRGV..IERLMEC....FESRAIPFTMRSLGEEMKDELERLMPEKFEFIYNR
10 YF...YPIGKRP.HECV..KELL---....--KLEKNLRFHSLTLGQKDDLKDNFVGVFDFTYNR
11 VF...YPLGAGD.KKPI..IESLIQF....YKDLSLPLELHSLQSNEVEELESYFPHTFEITQRR
12 YF...YPIGKRA.HACV..KELL---....--KLEKNLKFHSLTSEQKDDLRDNFVGVFDFTYNR
13 QFtqpIGYEKEN.LKEI..VDELIKY....RQKHNMDYLFKDAEEEFVKDFKELYDNNFTIEEDR
14 SI...LPLAKKDkLPEV..VDFVLEY....FSKNNKKIYLRGITTEVVEFLKEKYPGRFEYIEER
15 YL...FPVGADP.EQVVaaAHRLKAE....VVHEDYPLIFMGVTPDIHRCIEEHCSAEYYFIEDE
16 YY...MPIPKND.TPKN..IEKMKEK....IREILKENVAIHY---FTEYWYEKLKDDFNLQEKR
17 YF...MQPIGAD.KSKI..ADITLKLntlrKNNPDFKYLYGDVETPFLEQLHENFGNLVTSHEDK
18 WA...PVGPWGD.IDWA..SCTC---....---LGKGMEFIRVPEELASLWREVLGDRVTVQETP
19 YY...MPIPKND.TPEN..IEKMKEK....IREILKENVAINY---FTEYWYEKLKDDFNLQEKR
20 FH...PPIGPRD.PELM..-RELIQL....AMKVSDNTPLIFIDPDTALWIRELEPDLELVPDRD
21 FLhgpVGVDTNK.LPIV..IEKAKKY....FETQGYKFMLKRASQKTIDMLTQCGMKFESLLER-
22 YF...LPPLGGD.VAGA..LRVL---....---LDAGMTLYGADEPFVSRY--LAVGGVAVEEDR
23 YA...LPPLSGD.VTGA..LRTL---....---LADGFTIYGADDTFLERH--GADAAITVEEDR
20
|
1 AYAD
2 AYAD
3 DYAD
4 DYAD
5 DSFD
6 DSFD
7 DRSD
8 DRSD
9 DRSD
10 DRSD
11 DRFD
12 DRSD
13 DNAD
14 DLFD
15 AYCD
16 DYED
17 NNFD
18 GQWD
19 DYED
20 ----
21 ----
22 DAFD
23 DGFD